Improved systems and methods for removing the load of perchlorate and other oxyanions off of ion exchange resins through bioregeneration are disclosed. The improved systems and methods rely upon direct contact between the resin and a liquid product containing enrichment cultures of or pure strains of perchlorate-destroying microorganisms. Controlled temperatures also lead to improvements as do upflow conditions leading to bed expansion. These methods can be incorporated into methods for removing perchlorate from aqueous streams.